Error Probability Phred
Convert error probabilities in (0,1] to Phred quality scores.
Description
Phred quality uses a logarithmic scale for error probability.
Phred quality uses a logarithmic scale for error probability. Lower probabilities correspond to higher scores.1
Convert error probabilities in (0,1] to Phred quality scores.
When to use Error Probability Phred
Use this for the following task: Convert error probabilities in (0,1] to Phred quality scores.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Error Probability Phred and understand its results
- Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
- Enter errorProbabilities using the field table, then run the tool.
- Read phredScores. Interpret flags, units, ordering and placeholder values using the rules below.
- Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.
| Input field | Meaning | Value type and bounds | Requirement |
|---|---|---|---|
| errorProbabilities | Error probabilities | list of number; minimum entries 1; maximum entries 100000; each entry: number; greater than 0; maximum 1 | Required |
Supply a nonempty probability list in (0,1]. Return scores in input order, explicitly producing zero for probability one.2
Q = −10 log10(errorProbability) This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| phredScores | Phred scores | list of number |
{
"input": {
"errorProbabilities": [
0.1,
0.01,
0.001
]
},
"output": {
"phredScores": [
10,
20,
30
]
}
}Limitations and assumptions
Zero probability is rejected because it would require infinite quality. These scores are computed from supplied probabilities, not measured from reads.
The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.
Alternative or Complementary methods
Choose MAPQ Filter Fraction for this operation: Filter SAM mapping qualities by threshold while treating MAPQ 255 as unavailable. For a complementary task, use Trailing Adapter Contamination for this operation: Detect read-terminal matches to an adapter prefix above the chosen minimum match length.
Further background: Background specification: Error Probability Phred.
References
-
Background specification: Error Probability Phred — GA4GH / HTS specifications
-
Error Probability Phred — tool.io
Similar or alternative tools
- MAPQ Filter Fraction
Filter SAM mapping qualities by threshold while treating MAPQ 255 as unavailable.
- Trailing Adapter Contamination
Detect read-terminal matches to an adapter prefix above the chosen minimum match length.